--- a
+++ b/docs/api/user.md
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+# User
+
+## Benchmarking
+
+```{eval-rst}
+.. module:: nichecompass.benchmarking
+.. currentmodule:: nichecompass
+
+.. autosummary::
+    :toctree: generated
+
+    benchmarking.compute_benchmarking_metrics
+    benchmarking.compute_cas
+    benchmarking.compute_clisis
+    benchmarking.compute_gcs
+    benchmarking.compute_mlami
+    benchmarking.compute_nasw
+```
+
+## Data
+```{eval-rst}
+.. module:: nichecompass.data
+.. currentmodule:: nichecompass
+
+.. autosummary::
+    :toctree: generated
+
+    data.load_spatial_adata_from_csv
+```
+
+## Models
+
+```{eval-rst}
+.. module:: nichecompass.models
+.. currentmodule:: nichecompass
+
+.. autosummary::
+    :toctree: generated
+
+    models.NicheCompass
+```
+
+## Gene Program Utilities
+
+```{eval-rst}
+.. module:: nichecompass.utils
+.. currentmodule:: nichecompass
+
+.. autosummary::
+    :toctree: generated
+
+    utils.add_gps_from_gp_dict_to_adata
+    utils.add_multimodal_mask_to_adata
+    utils.extract_gp_dict_from_collectri_tf_network
+    utils.extract_gp_dict_from_nichenet_lrt_interactions
+    utils.extract_gp_dict_from_mebocost_es_interactions
+    utils.extract_gp_dict_from_omnipath_lr_interactions
+    utils.filter_and_combine_gp_dict_gps
+    utils.get_gene_annotations
+    utils.generate_multimodal_mapping_dict
+    utils.get_unique_genes_from_gp_dict
+    utils.generate_enriched_gp_info_plots
+```
+
+## Cell-Cell Communication Utilities
+
+```{eval-rst}
+.. module:: nichecompass.utils
+.. currentmodule:: nichecompass
+
+.. autosummary::
+    :toctree: generated
+
+    utils.compute_communication_gp_network
+    utils.visualize_communication_gp_network
+```
+
+## Other Utilities
+```{eval-rst}
+.. module:: nichecompass.utils
+.. currentmodule:: nichecompass
+
+.. autosummary::
+    :toctree: generated
+
+    utils.create_new_color_dict
+```